The robustness of some Carboniferous fossil leaf venation networks to simulated damage.

Biological networks vary widely in their architecture and functional properties. Branching networks are good for transportation efficiency, while networks including loops offer good resistance to damage, and examples of these two topologies are found in leaf venation networks. The first plants with reticulate (loopy) leaf venation evolved in the Pennsylvanian of the Carboniferous, but the responses of different venation network architectures from this time period to damage are currently largely unknown. Here we address this issue with a computational analysis of venation network robustness that is focused on fossil leaves from the Pennsylvanian. We attacked fossil venation networks with simulated damage to individual vein segments and leaf blades. For both types of attack, branched venation networks are the least robust to damage, with greater robustness shown by the net-like reticulate networks found in the Pennsylvanian. A living angiosperm Betula alba was the most robust in our analysis. This may highlight a role for resistance to damage in the evolution of reticulate leaf venation in the Carboniferous, but further work is needed to answer the broader question of why reticulate leaf venation first evolved in the Pennsylvanian.

The fossil insect assemblage associated with the Toarcian (Lower Jurassic) oceanic anoxic event from Alderton Hill, Gloucestershire, UK.

Extreme global warming and environmental changes associated with the Toarcian (Lower Jurassic) Oceanic Anoxic Event (T-OAE, ~183 Mya) profoundly impacted marine organisms and terrestrial plants. Despite the exceptionally elevated abundances of fossil insects from strata of this age, only assemblages from Germany and Luxembourg have been studied in detail. Here, we focus on the insect assemblage found in strata recording the T-OAE at Alderton Hill, Gloucestershire, UK, where <15% of specimens have previously been described. We located all known fossil insects (n = 370) from Alderton Hill, and used these to create the first comprehensive taxonomic and taphonomic analysis of the entire assemblage. We show that a diverse palaeoentomofaunal assemblage is preserved, comprising 12 orders, 21 families, 23 genera and 21 species. Fossil disarticulation is consistent with insect decay studies. The number of orders is comparable with present-day assemblages from similar latitudes (30°-40°N), including the Azores, and suggests that the palaeoentomofauna reflects a life assemblage. At Alderton, Hemiptera, Coleoptera and Orthoptera are the commonest (56.1%) orders. The high abundance of Hemiptera (22.1%) and Orthoptera (13.4%) indicates well-vegetated islands, while floral changes related to the T-OAE may be responsible for hemipteran diversification. Predatory insects are relatively abundant (~10% of the total assemblage) and we hypothesise that the co-occurrence of fish and insects within the T-OAE represents a jubilee-like event. The marginally higher proportion of sclerotised taxa compared to present-day insect assemblages possibly indicates adaptation to environmental conditions or taphonomic bias. The coeval palaeoentomofauna from Strawberry Bank, Somerset is less diverse (9 orders, 12 families, 6 genera, 3 species) and is taphonomically biased. The Alderton Hill palaeoentomofauna is interpreted to be the best-preserved and most representative insect assemblage from Toarcian strata in the UK. This study provides an essential first step towards understanding the likely influence of the T-OAE on insects.

Quantifying the complexity of plant reproductive structures reveals a history of morphological and functional integration.

Vascular plant reproductive structures have undoubtedly become more complex through time, evolving highly differentiated parts that interact in specialized ways. But quantifying these patterns at broad scales is challenging because lineages produce disparate reproductive structures that are often difficult to compare and homologize. We develop a novel approach for analysing interactions within reproductive structures using networks, treating component parts as nodes and a suite of physical and functional interactions among parts as edges. We apply this approach to the plant fossil record, showing that interactions have generally increased through time and that the concentration of these interactions has shifted towards differentiated surrounding organs, resulting in more compact, functionally integrated structures. These processes are widespread across plant lineages, but their extent and timing vary with reproductive biology; in particular, seed-producing structures show them more strongly than spore or pollen-producing structures. Our results demonstrate that major reproductive innovations like the origin of seeds and angiospermy were associated with increased integration through greater interactions among parts. But they also reveal that for certain groups, particularly Mesozoic gymnosperms, millions of years elapsed between the origin of reproductive innovations and increased interactions among parts within their reproductive structures.

Geometric and topological approaches to shape variation in Ginkgo leaves.

Leaf shape is a key plant trait that varies enormously. The range of applications for data on this trait requires frequent methodological development so that researchers have an up-to-date toolkit with which to quantify leaf shape. We generated a dataset of 468 leaves produced by Ginkgo biloba, and 24 fossil leaves produced by evolutionary relatives of extant Ginkgo. We quantified the shape of each leaf by developing a geometric method based on elastic curves and a topological method based on persistent homology. Our geometric method indicates that shape variation in modern leaves is dominated by leaf size, furrow depth and the angle of the two lobes at the leaf base that is also related to leaf width. Our topological method indicates that shape variation in modern leaves is dominated by leaf size and furrow depth. We have applied both methods to modern and fossil material: the methods are complementary, identifying similar primary patterns of variation, but also revealing different aspects of morphological variation. Our topological approach distinguishes long-shoot leaves from short-shoot leaves, both methods indicate that leaf shape influences or is at least related to leaf area, and both could be applied in palaeoclimatic and evolutionary studies of leaf shape.

Reproductive innovations and pulsed rise in plant complexity.

Morphological complexity is a notable feature of multicellular life, although whether it evolves gradually or in early bursts is unclear. Vascular plant reproductive structures, such as flowers, are familiar examples of complex morphology. In this study, we use a simple approach based on the number of part types to analyze changes in complexity over time. We find that reproductive complexity increased in two pulses separated by ~250 million years of stasis, including an initial rise in the Devonian with the radiation of vascular plants and a pronounced increase in the Late Cretaceous that reflects flowering plant diversification. These pulses are associated with innovations that increased functional diversity, suggesting that shifts in complexity are linked to changes in function regardless of whether they occur early or late in the history of vascular plants.

Measuring Biodiversity and Extinction-Present and Past.

How biodiversity is changing in our time represents a major concern for all organismal biologists. Anthropogenic changes to our planet are decreasing species diversity through the negative effects of pollution, habitat destruction, direct extirpation of species, and climate change. But major biotic changes-including those that have both increased and decreased species diversity-have happened before in Earth's history. Biodiversity dynamics in past eras provide important context to understand ecological responses to current environmental change. The work of assessing biodiversity is woven into ecology, environmental science, conservation, paleontology, phylogenetics, evolutionary and developmental biology, and many other disciplines; yet, the absolute foundation of how we measure species diversity depends on taxonomy and systematics. The aspiration of this symposium, and complementary contributed talks, was to promote better understanding of our common goals and encourage future interdisciplinary discussion of biodiversity dynamics. The contributions in this collection of papers bring together a diverse group of speakers to confront several important themes. How can biologists best respond to the urgent need to identify and conserve diversity? How can we better communicate the nature of species across scientific disciplines? Where are the major gaps in knowledge about the diversity of living animal and plant groups, and what are the implications for understanding potential diversity loss? How can we effectively use the fossil record of past diversity and extinction to understand current biodiversity loss?

The Latitudinal Distribution of Morphological Diversity among Holocene Angiosperm Pollen Grains from Eastern North America and the Neotropics.

Current knowledge about the biogeographic patterns of biodiversity is based mostly on taxonomic diversity, which is typically measured as the number of species or higher taxa. In this paper I analyze 26 previously published Holocene lake core pollen records in order to assess how the morphological diversity of angiosperm pollen grains varies with latitude on a transect that includes eastern North America and the Neotropics. This represents a step toward understanding the evolution of plant morphology in a biogeographical context. I employ a system of eight discrete characters to describe first-order features of angiosperm pollen morphology and use algorithms written in the Python programming language to assess their morphological diversity. There is no statistically significant relationship between taxonomic diversity and morphological diversity in the samples of Holocene angiosperm pollen investigated here. The number of pollen morphotypes in the sediment samples investigated here increases from high latitudes to the tropics, but the highest morphological diversity occurs at high latitudes, and the lowest morphological diversity occurs at mid-latitudes around 40-50°N. At the biome level, there are peaks in morphological diversity at low and high latitudes with a trough in mid latitudes. There is evidence of high levels of pollen morphotype endemism in the tropical biome, and further work on how the volume of morphological space varies with latitude is needed in order to understand whether taxa in species-rich tropical ecosystems are more densely packed into morphological space.

The influence of environmental forcing on biodiversity and extinction in a resource competition model.

In this paper, we study a model of many species that compete, directly or indirectly, for a pool of common resources under the influence of periodic, stochastic, and/or chaotic environmental forcing. Using numerical simulations, we find the number and sequence of species going extinct when the community is initially packed with a large number of species of random initial densities. Thereby, any species with a density below a given threshold is regarded to be extinct.

Comparative performance of airyscan and structured illumination superresolution microscopy in the study of the surface texture and 3D shape of pollen.

The visualization of taxonomically diagnostic features of individual pollen grains can be a challenge for many ecologically and phylogenetically important pollen types. The resolution of traditional optical microscopy is limited by the diffraction of light (250 nm), while high resolution tools such as electron microscopy are limited by laborious preparation and imaging workflows. Airyscan confocal superresolution and structured illumination superresolution (SR-SIM) microscopy are powerful new tools for the study of nanoscale pollen morphology and three-dimensional structure that can overcome these basic limitations. This study demonstrates their utility in capturing morphological details below the diffraction limit of light. Using three distinct pollen morphotypes (Croton hirtus, Dactylis glomerata, and Helianthus sp.) and contrast-enhancing fluorescent staining, we were able to assess the effectiveness of the Airyscan and SR-SIM. We further demonstrate that these new superresolution methods can be easily applied to the study of fossil pollen material.

A morphometric analysis of vegetation patterns in dryland ecosystems.

Vegetation in dryland ecosystems often forms remarkable spatial patterns. These range from regular bands of vegetation alternating with bare ground, to vegetated spots and labyrinths, to regular gaps of bare ground within an otherwise continuous expanse of vegetation. It has been suggested that spotted vegetation patterns could indicate that collapse into a bare ground state is imminent, and the morphology of spatial vegetation patterns, therefore, represents a potentially valuable source of information on the proximity of regime shifts in dryland ecosystems. In this paper, we have developed quantitative methods to characterize the morphology of spatial patterns in dryland vegetation. Our approach is based on algorithmic techniques that have been used to classify pollen grains on the basis of textural patterning, and involves constructing feature vectors to quantify the shapes formed by vegetation patterns. We have analysed images of patterned vegetation produced by a computational model and a small set of satellite images from South Kordofan (South Sudan), which illustrates that our methods are applicable to both simulated and real-world data. Our approach provides a means of quantifying patterns that are frequently described using qualitative terminology, and could be used to classify vegetation patterns in large-scale satellite surveys of dryland ecosystems.

A combinatorial approach to angiosperm pollen morphology.

Angiosperms (flowering plants) are strikingly diverse. This is clearly expressed in the morphology of their pollen grains, which are characterized by enormous variety in their shape and patterning. In this paper, I approach angiosperm pollen morphology from the perspective of enumerative combinatorics. This involves generating angiosperm pollen morphotypes by algorithmically combining character states and enumerating the results of these combinations. I use this approach to generate 3 643 200 pollen morphotypes, which I visualize using a parallel-coordinates plot. This represents a raw morphospace. To compare real-world and theoretical morphologies, I map the pollen of 1008 species of Neotropical angiosperms growing on Barro Colorado Island (BCI), Panama, onto this raw morphospace. This highlights that, in addition to their well-documented taxonomic diversity, Neotropical rainforests also represent an enormous reservoir of morphological diversity. Angiosperm pollen morphospace at BCI has been filled mostly by pollen morphotypes that are unique to single plant species. Repetition of pollen morphotypes among higher taxa at BCI reflects both constraint and convergence. This combinatorial approach to morphology addresses the complexity that results from large numbers of discrete character combinations and could be employed in any situation where organismal form can be captured by discrete morphological characters.

Evidence for coal forest refugia in the seasonally dry Pennsylvanian tropical lowlands of the Illinois Basin, USA.

The Moscovian plant macroflora at Cottage Grove southeastern Illinois, USA, is a key example of Pennsylvanian (323-299 Million years ago) dryland vegetation. There is currently no palynological data from the same stratigraphic horizons as the plant macrofossils, leaves and other vegetative and reproductive structures, at this locality. Consequently, reconstructions of the standing vegetation at Cottage Grove from these sediments lack the complementary information and a more regional perspective that can be provided by sporomorphs (prepollen, pollen, megaspores and spores). In order to provide this, we have analysed the composition of fossil sporomorph assemblages in two rock samples taken from macrofossil-bearing inter-coal shale at Cottage Grove. Our palynological data differ considerably in composition and in the dominance-diversity profile from the macrofossil vegetation at this locality. Walchian conifers and pteridosperms are common elements in the macroflora, but are absent in the sporomorph assemblages. Reversely, the sporomorph assemblages at Cottage Grove comprise 17 spore taxa (∼16% and ∼63% of the total assemblages) that are known from the lycopsid orders Isoetales, Lepidodendrales and Selaginallales, while Cottage Grove's macrofloral record fails to capture evidence of a considerable population of coal forest lycopsids. We interpret our results as evidence that the Pennsylvanian dryland glacial landscape at Cottage Grove included fragmented populations of wetland plants living in refugia.

Accuracy and consistency of grass pollen identification by human analysts using electron micrographs of surface ornamentation.

PREMISE OF THE STUDY: Humans frequently identify pollen grains at a taxonomic rank above species. Grass pollen is a classic case of this situation, which has led to the development of computational methods for identifying grass pollen species. This paper aims to provide context for these computational methods by quantifying the accuracy and consistency of human identification. • METHODS: We measured the ability of nine human analysts to identify 12 species of grass pollen using scanning electron microscopy images. These are the same images that were used in computational identifications. We have measured the coverage, accuracy, and consistency of each analyst, and investigated their ability to recognize duplicate images. • RESULTS: Coverage ranged from 87.5% to 100%. Mean identification accuracy ranged from 46.67% to 87.5%. The identification consistency of each analyst ranged from 32.5% to 87.5%, and each of the nine analysts produced considerably different identification schemes. The proportion of duplicate image pairs that were missed ranged from 6.25% to 58.33%. • DISCUSSION: The identification errors made by each analyst, which result in a decline in accuracy and consistency, are likely related to psychological factors such as the limited capacity of human memory, fatigue and boredom, recency effects, and positivity bias.

Classification of grass pollen through the quantitative analysis of surface ornamentation and texture.

Taxonomic identification of pollen and spores uses inherently qualitative descriptions of morphology. Consequently, identifications are restricted to categories that can be reliably classified by multiple analysts, resulting in the coarse taxonomic resolution of the pollen and spore record. Grass pollen represents an archetypal example; it is not routinely identified below family level. To address this issue, we developed quantitative morphometric methods to characterize surface ornamentation and classify grass pollen grains. This produces a means of quantifying morphological features that are traditionally described qualitatively. We used scanning electron microscopy to image 240 specimens of pollen from 12 species within the grass family (Poaceae). We classified these species by developing algorithmic features that quantify the size and density of sculptural elements on the pollen surface, and measure the complexity of the ornamentation they form. These features yielded a classification accuracy of 77.5%. In comparison, a texture descriptor based on modelling the statistical distribution of brightness values in image patches yielded a classification accuracy of 85.8%, and seven human subjects achieved accuracies between 68.33 and 81.67%. The algorithmic features we developed directly relate to biologically meaningful features of grass pollen morphology, and could facilitate direct interpretation of unsupervised classification results from fossil material.

Aberrant Classopollis pollen reveals evidence for unreduced (2n) pollen in the conifer family Cheirolepidiaceae during the Triassic-Jurassic transition.

Polyploidy (or whole-genome doubling) is a key mechanism for plant speciation leading to new evolutionary lineages. Several lines of evidence show that most species among flowering plants had polyploidy ancestry, but it is virtually unknown for conifers. Here, we study variability in pollen tetrad morphology and the size of the conifer pollen type Classopollis extracted from sediments of the Triassic-Jurassic transition, 200 Ma. Classopollis producing Cheirolepidiaceae were one of the most dominant and diverse groups of conifers during the Mesozoic. We show that aberrant pollen Classopollis tetrads, triads and dyads, and the large variation in pollen size indicates the presence of unreduced (2n) pollen, which is one of the main mechanisms in modern polyploid formation. Polyploid speciation may explain the high variability of growth forms and adaptation of these conifers to different environments and their resistance to extreme growth conditions. We suggest that polyploidy may have also reduced the extinction risk of these conifers during the End-Triassic biotic crisis.

Tracking taphonomic regimes using chemical and mechanical damage of pollen and spores: an example from the Triassic-Jurassic mass extinction.

The interpretation of biotic changes in the geological past relies on the assumption that samples from different time intervals represent an equivalent suite of natural sampling conditions. As a result, detailed investigations of taphonomic regimes during intervals of major biotic upheaval, such as mass extinctions, are crucial. In this paper, we have used variations in the frequency of chemical and mechanical sporomorph (pollen and spore) damage as a guide to taphonomic regimes across the Triassic-Jurassic mass extinction (Tr-J; ∼201.3 Ma) at a boundary section at Astartekløft, East Greenland. We find that the frequency of sporomorph damage is extremely variable in samples from this locality. This likely reflects a combination of taxon-specific susceptibility to damage and the mixing of sporomorphs from a mosaic of environments and taphonomic regimes. The stratigraphic interval containing evidence of plant extinction and compositional change in the source vegetation at Astartekløft is not marked by a consistent rise or fall in the frequency of sporomorph damage. This indicates that natural taphonomic regimes did not shift radically during this critical interval. We find no evidence of a consistent relationship between the taxonomic richness of sporomorph assemblages and the frequency of damage among sporomorphs at Astartekløft. This indicates that previously reported patterns of sporomorph richness across the Tr-J at this locality are likely to be robust. Taken together, our results suggest that the patterns of vegetation change at Astartekløft represent a real biological response to environmental change at the Tr-J.

Capturing the surface texture and shape of pollen: a comparison of microscopy techniques.

Research on the comparative morphology of pollen grains depends crucially on the application of appropriate microscopy techniques. Information on the performance of microscopy techniques can be used to inform that choice. We compared the ability of several microscopy techniques to provide information on the shape and surface texture of three pollen types with differing morphologies. These techniques are: widefield, apotome, confocal and two-photon microscopy (reflected light techniques), and brightfield and differential interference contrast microscopy (DIC) (transmitted light techniques). We also provide a first view of pollen using super-resolution microscopy. The three pollen types used to contrast the performance of each technique are: Croton hirtus (Euphorbiaceae), Mabea occidentalis (Euphorbiaceae) and Agropyron repens (Poaceae). No single microscopy technique provided an adequate picture of both the shape and surface texture of any of the three pollen types investigated here. The wavelength of incident light, photon-collection ability of the optical technique, signal-to-noise ratio, and the thickness and light absorption characteristics of the exine profoundly affect the recovery of morphological information by a given optical microscopy technique. Reflected light techniques, particularly confocal and two-photon microscopy, best capture pollen shape but provide limited information on very fine surface texture. In contrast, transmitted light techniques, particularly differential interference contrast microscopy, can resolve very fine surface texture but provide limited information on shape. Texture comprising sculptural elements that are spaced near the diffraction limit of light (~250 nm; NDL) presents an acute challenge to optical microscopy. Super-resolution structured illumination microscopy provides data on the NDL texture of A. repens that is more comparable to textural data from scanning electron microscopy than any other optical microscopy technique investigated here. Maximizing the recovery of morphological information from pollen grains should lead to more robust classifications, and an increase in the taxonomic precision with which ancient vegetation can be reconstructed.

An explanation for conflicting records of Triassic-Jurassic plant diversity.

Macrofossils (mostly leaves) and sporomorphs (pollen and spores) preserve conflicting records of plant biodiversity during the end-Permian (P-Tr), Triassic-Jurassic (Tr-J), and end-Cretaceous (K-T) mass extinctions. Estimates of diversity loss based on macrofossils are typically much higher than estimates of diversity loss based on sporomorphs. Macrofossils from the Tr-J of East Greenland indicate that standing species richness declined by as much as 85% in the Late Triassic, whereas sporomorph records from the same region, and from elsewhere in Europe, reveal little evidence of such catastrophic diversity loss. To understand this major discrepancy, we have used a new high-resolution dataset of sporomorph assemblages from Astartekløft, East Greenland, to directly compare the macrofossil and sporomorph records of Tr-J plant biodiversity. Our results show that sporomorph assemblages from the Tr-J boundary interval are 10-12% less taxonomically diverse than sporomorph assemblages from the Late Triassic, and that vegetation composition changed rapidly in the boundary interval as a result of emigration and/or extirpation of taxa rather than immigration and/or origination of taxa. An analysis of the representation of different plant groups in the macrofossil and sporomorph records at Astartekløft reveals that reproductively specialized plants, including cycads, bennettites and the seed-fern Lepidopteris are almost absent from the sporomorph record. These results provide a means of reconciling the macrofossil and sporomorph records of Tr-J vegetation change, and may help to understand vegetation change during the P-Tr and K-T mass extinctions and around the Paleocene-Eocene Thermal Maximum.